8C6H

Light SFX structure of D.m(6-4)photolyase at 2ps time delay


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.

Cellini, A.Shankar, M.K.Nimmrich, A.Hunt, L.A.Monrroy, L.Mutisya, J.Furrer, A.Beale, E.V.Carrillo, M.Malla, T.N.Maj, P.Vrhovac, L.Dworkowski, F.Cirelli, C.Johnson, P.J.M.Ozerov, D.Stojkovic, E.A.Hammarstrom, L.Bacellar, C.Standfuss, J.Maj, M.Schmidt, M.Weinert, T.Ihalainen, J.A.Wahlgren, W.Y.Westenhoff, S.

(2024) Nat Chem 16: 624-632

  • DOI: https://doi.org/10.1038/s41557-023-01413-9
  • Primary Citation of Related Structures:  
    8C1U, 8C69, 8C6A, 8C6B, 8C6C, 8C6F, 8C6H

  • PubMed Abstract: 

    Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-1500Drosophila melanogasterMutation(s): 0 
Gene Names: phr6-4CG2488
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster)
Go to UniProtKB:  Q8SXK5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.9α = 90
b = 103.9β = 90
c = 52.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references